FIMO Results

FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]

DATABASE AND MOTIFS

  DATABASE /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/BY4742--RIM101.fa
  
  Database contains 551 sequences, 407065 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        AAAAAWAW
        8
        AAAAAAAT
       
        ACCRACT
        7
        ACCAACT
       
        CABACGC
        7
        CATACGC
       
        AAGGCGM
        7
        AAGGCGC
       
        CGSCCA
        6
        CGCCCA
       
        GGATCRAA
        8
        GGATCGAA
       
        ACCCABAC
        8
        ACCCACAC
       
        GYGCCAGA
        8
        GTGCCAGA
       
        AAAAAGAA
        8
        AAAAAGAA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TGTTGWA
        7
        TGTTGAA
       
        CCAACWGA
        8
        CCAACTGA
       
        CCRTGGAG
        8
        CCGTGGAG
       
        GGTCAGAA
        8
        GGTCAGAA
       
        TCKCAAGA
        8
        TCTCAAGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
AAAAAWAW	8	AAAAAAAT
ACCRACT	7	ACCAACT
CABACGC	7	CATACGC
AAGGCGM	7	AAGGCGC
CGSCCA	6	CGCCCA
GGATCRAA	8	GGATCGAA
ACCCABAC	8	ACCCACAC
GYGCCAGA	8	GTGCCAGA
AAAAAGAA	8	AAAAAGAA
ATGGCAWC	8	ATGGCAAC
TGTTGWA	7	TGTTGAA
CCAACWGA	8	CCAACTGA
CCRTGGAG	8	CCGTGGAG
GGTCAGAA	8	GGTCAGAA
TCKCAAGA	8	TCTCAAGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 27 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the tab-delimited plain text output file fimo.txt, the GFF file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
The table is sorted by increasing p-value.

Motif ID	Alt ID	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence
GGTCAGAA	DREME-16	chrVIII	-	79	86	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXIII	-	96	103	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXII	-	120	127	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrIX	-	124	131	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXII	-	5769	5776	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrVIII	-	34995	35002	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrIX	-	324350	324357	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrIX	-	336396	336403	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrIV	-	340701	340708	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrX	-	374471	374478	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXI	-	513379	513386	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrVII	-	544624	544631	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrIV	-	1305890	1305897	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXV	+	80835	80842	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXIII	+	146819	146826	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrX	+	204750	204757	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrX	+	355471	355478	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrII	+	405975	405982	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXII	+	427147	427154	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXIII	+	463569	463576	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrVII	+	531625	531632	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrX	+	541523	541530	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrVIII	+	562403	562410	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrIV	+	568979	568986	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXV	+	571973	571980	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXII	+	793933	793940	1.2e-05	0.36	GGTCAGAA
GGTCAGAA	DREME-16	chrXV	+	1091219	1091226	1.2e-05	0.36	GGTCAGAA

DEBUGGING INFORMATION

Command line:

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/background --motif GGTCAGAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/BY4742--RIM101.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/BY4742--RIM101.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/background
    alphabet = DNA
    max stored scores = 100000
  
  
    allow clobber = true
    compute q-values = true
    parse genomic coord. = true
  
  
    text only = false
    scan both strands = true
    max strand = false
  
  
    threshold type = p-value
    output theshold = 0.0001
    pseudocount = 0.1
  
  
    alpha = 1
    verbosity = 1

This information can be useful in the event you wish to report a problem with the FIMO software.

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output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/BY4742--RIM101.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RIM101/background	alphabet = DNA	max stored scores = 100000
allow clobber = true	compute q-values = true	parse genomic coord. = true
text only = false	scan both strands = true	max strand = false
threshold type = p-value	output theshold = 0.0001	pseudocount = 0.1
alpha = 1	verbosity = 1